Windows Server 2012 R2, cannot install any role or features using GUI Server manager

This sounds like an issue with the OS installation. If possible, I would run a sfc /scannow on the server and see if that corrects it. If not, toss the OS CD in there and run a repair from that.

Use setspn to manually create the SPN https://technet.microsoft.com/en-us/library/dd348559%28v=ws.10%29.aspx

SETSPN -A WSMAN/{server-short-name}{domainshortname\server-short-name}
SETSPN -A WSMAN/{server-FQDN-name.}{domainshortname\server-short-name}

This is usually due to a GPO setting in Windows Remote Management. As soon as you set the "Allow Remote Shell Access" to Not Configured it should work. Computer Configuration\Administrative Templates\Windows Components\Windows Remote Shell.